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Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

Count multiplier for DEG analysis: 10000x
This is to counter zeros

TES dynamics

Those reads were counted only, where the 3-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

hclust

Assigning genes to clusters

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 5 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

All ORFs - Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Clustered ORFs only - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combine Kinetic classes

De Novo - Significant

De Novo - All clusters

Literature clusters